Genotype concordance and polygenic risk score estimation across consumer genetic testing data.

Area of Science:

• Genomics
• Bioinformatics
• Personalized Medicine

Background:

• The consumer genomics industry is rapidly expanding, providing genetic insights to millions.
• Understanding the comparability of data from various direct-to-consumer (DTC) genetic testing services is crucial.

Purpose of the Study:

• To evaluate genotype concordance and genetic risk estimation across different consumer genomics platforms.
• To identify potential discrepancies in genetic information derived from SNP-array and whole-genome sequencing services.

Main Methods:

• Comparative analysis of genotyped sites from two SNP-array and one low-pass whole-genome sequencing DTC services.
• Assessment of genotype concordance for overlapping sites.
• Evaluation of genetic risk scores, including APOE genotyping for Alzheimer's disease.

Main Results:

• The three services predominantly genotyped distinct sets of genetic markers.
• High concordance (99.6%) was observed between two SNP-array services, but lower concordance (73.0%) with the sequencing service.
• Discrepancies led to varied APOE genotypes and Alzheimer's disease genetic risk scores.

Conclusions:

• Genotype data from different consumer genomics platforms can yield differing genetic risk estimates.
• Careful quality control and interpretation are essential when using DTC genetic data.
• The heterogeneity of DTC genomic data necessitates standardized validation protocols.